TTs will cycle back to back, just like CRFs will, but the extra benefit in TT2 over the 1 shot benefit in BO2 supports the move to BO1, at least in my mind. And this way, if you ever put a torp on there, you can switch that out to HY1 without having to retrain 2 skills.

APO1 can be replaced by any AP of your choice - which ever works best for you, but with AP doffs to reduce cooldown APO is probably the best.